Arthrobacter crusticola sp. nov., Isolated from Biological Soil Crusts in the Mu Us Sandy Land, China.

Mu Us Sandy Land in China is a very fragile ecological environment due to serious desertification. While attempting to gain insights into the biodiversity of biological soil crusts of Mu Us Sandy Land, a novel bacterial strain, SLN-3T, was isolated. It was phylogenetically placed into the genus Arthrobacter within the family Micrococcaceae based on its 16S rRNA gene sequence. The most closely related species were Arthrobacter ruber MDB1-42T (98.6%) and Arthrobacter agilis DSM 20550T (98.3%). Cells of the novel species were Gram-stain-positive, aerobic, and non-endospore-forming. The values of average nucleotide identity and the digital DNA-DNA hybridization between SLN-3T and MDB1-42T were 84.9% and 21.3%, respectively. The draft genome size of strain SLN-3T was 3.67 Mb, and its genomic G+C content was 68.1%. The predominant cellular fatty acids were anteiso-C15:0 and C17:0 anteiso. Glucose, galactose, and ribose were the whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipid, and phospholipid. The peptidoglycan contained lysine, glutamic acid, and alanine. The predominant menaquinone was MK-9(H2). Based on the data from the chemotaxonomic, phylogenetic, and phenotypic evidence, a novel species named Arthrobacter crusticola sp. nov is proposed, whose type strain is SLN-3T (= ACCC 61595T = JCM 33723T).

Phytohalomonas tamaricis gen. nov., sp. nov., an endophytic bacterium isolated from Tamarix ramosissima roots growing in Kumtag desert.

A gram-stain-negative, aerobic, non-spore-forming, rod-shaped, non-motile bacterium strain R4HLG17T was isolated from Tamarix ramosissima roots growing in Kumtag desert. The strain grew at salinities of 0-16% (w/v) NaCl (optimum 5-6%), pH 5-9 (optimum 7) and at 16-45 °C. Based on 16S rRNA gene sequence similarity, strain R4HLG17T belonged to the family Halomonadaceae and was most closely related to Halomonas lutea DSM 23508T(95.1%), followed by Halotalea alkalilenta AW-7T(94.8%), Salinicola acroporae S4-41T(94.8%), Salinicola halophilus CG4.1T(94.6%), and Larsenimonas salina M1-18T(94.4%). Multilocus sequence analysis (MLSA) based on the partial sequences of 16S rRNA, atpA, gyrB, rpoD, and secA genes indicated that the strain R4HLG17T formed an independent and monophyletic branch related to other genera of Halomonadaceae, supporting its placement as a new genus in this family. The draft genome of strain R4HLG17T was 3.6 Mb with a total G + C content of 55.1%. The average nucleotide identity to Halomonas lutea DSM 23508T was 83.5%. Q-9 was detected as the major respiratory quinone and summed feature 8 (C18:1ω7c/C18:1ω6c), summed feature 3 (C16:1ω7c/C16:1ω6c), and C16:0 as predominant cellular fatty acids. On the basis of chemotaxonomic, phylogenetic, and phenotypic evidence, strain R4HLG17T is concluded to represent a novel species of a new genus within Halomonadaceae, for which the name Phytohalomonas tamaricis gen. nov., sp. nov., is proposed. The type strain is R4HLG17T (=ACCC 19929T=KCTC 52415T).

Rhizobium deserti sp. Nov Isolated from Biological Soil Crusts Collected at Mu Us Sandy Land, China.

A novel gram-negative, aerobic, non-spore-forming, rod-shaped, and non-nitrogen-fixing bacterium, named SPY-1T, was isolated from biological soil crusts collected at Mu Us Sandy Land, China. Based on 16S rRNA sequence similarity, strain SPY-1T was most closely related to Neorhizobium alkalisoli CCTCC AB 2014138T (98.7%), Neorhizobium huautlense CGMCC 1.2538T (98.6%), Neorhizobium galegae DSM 11542T (98.4%), Rhizobium wenxiniae 166T (97.9%), and Rhizobium smilacinae CCTCC AB 2013016T (97.5%). Phylogenetic analysis based on 16S rRNA sequencing and multilocus sequence analysis of partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain SPY-1T was a member of the genus Rhizobium. The draft genome of strain SPY-1T was 4.75 Mb in size, and the G + C content was 60.0%. The average nucleotide identity (ANI) values to N. alkalisoli CCTCC AB 2014138T and R. smilacinae CCTCC AB 2013016T were both 84.0%. The digital DNA-DNA hybridization (dDDH) values to N. alkalisoli CCTCC AB 2014138T and R. smilacinae CCTCC AB 2013016T were 20.9% and 20.2%, respectively. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C16:0. Based on the data from chemotaxonomic, phylogenetic, and phenotypic evidence, strain SPY-1T represents a novel species in the genus Rhizobium, for which the name Rhizobium deserti sp. nov. is proposed. The type strain is SPY-1T (= ACCC 61627T = JCM 33732T).

Neorhizobium lilium sp. nov., an endophytic bacterium isolated from Lilium pumilum bulbs in Hebei province.

A novel gram-negative, aerobic, non-spore-forming, rod-shaped and non-nitrogen fixing bacterium named strain 24NRT was isolated from wild Lilium pumilum bulbs in Fuping, Baoding City, Hebei province, PR China. The 16S rRNA gene sequences of strains 24NRT showed the highest similarity to Neorhizobium alkalisoli DSM 21826T (98.5%) and N. galegae HAMBI 540T (98.1%). Phylogenetic analysis based on 16S rRNA genes and multilocus sequence analysis (MLSA) based on the partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain 24NRT is a member of the genus Neorhizobium. The average nucleotide identity between the genome sequence of strain 24NRT and that of the isolate N. alkalisoli DSM 21826T was 83.1%, and the digital DNA-DNA hybridization was 20.1%. The G+C content of strain 24NRT was 60.3 mol %. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. Based on phenotypic, phylogenetic, and genotypic data, strain 24NRT is considered to represent a novel species of the genus Neorhizobium, for which the name Neorhizobium lilium sp. nov. is proposed. The type strain is 24NRT (= ACCC 61588T = JCM 33731T).

Global Methylomic and Transcriptomic Analyses Reveal the Broad Participation of DNA Methylation in Daily Gene Expression Regulation of Populus trichocarpa.

Changes in DNA methylation patterns in different tissues, at various developmental stages, and under environmental stimuli have been investigated in plants. However, the involvement of DNA methylation in daily gene expression regulation and the plant circadian clock have not been reported. Here, we investigated DNA methylomes and mRNA transcriptomes from leaves of P. trichocarpa over 24 h by high-throughput sequencing. We found that approximately 15.63-19.50% of the genomic cytosine positions were methylated in mature poplar leaves, with approximately half being in the form of asymmetric CHH sites. Repetitive sequences and transposable elements (TEs) were heavily methylated, and the hAT and CMC-EnSpm transposons were more heavily methylated than other TEs. High methylation levels were observed upstream and downstream of the transcribed region, medium in exon and intron, low in untranslated region (5'-UTR and 3'-UTR) of genic regions. In total, about 53,689 differentially methylated regions (DMRs) were identified and CHH context was the most abundant type among daily DNA methylation changes. The DMRs overlapped with over one third of the total poplar genes, including plant defense genes. In addition, a positive correlation between expression levels and DNA methylation levels in the gene body region were observed in DMR overlapping genes. About 1,895 circadian regulated genes overlapped with DMRs, with 871 hypermethylated genes with down-regulated expression levels and 881 hypomethylated genes with up-regulated expression levels, indicating the possible regulation of DNA methylation on the daily rhythmic expression of these genes. But rhythmic DNA methylation changes were not detected in any oscillator component genes controlling the plant circadian clock. Our results suggest that DNA methylation participates widely in daily gene expression regulation, but is not the main mechanism modulating the plant circadian clock.

Phyllobacterium phragmitis sp. nov., an endophytic bacterium isolated from Phragmites australis rhizome in Kumtag Desert.

A Gram-negative rod, designated strain 1N-3T, was isolated from a rhizome of Phragmites australis grown in Kumtag Desert, China. Phylogenetic analysis showed that the strain is closely related to Phyllobacterium salinisoli LMG 30173T with 99.0% sequence similarity in the 16S rRNA gene and 92.9% in the atpD gene. Growth was observed at salinities of 0-4% (w/v), over a pH range of 5.0-10.0 (optimum 8.0) and at temperatures of 15-40 °C (optimum 30 °C). The predominant cellular fatty acids were identified as summed feature 8 (C18:1ω7c/C18:1ω6c). The G+C content of strain 1N-3T was determined to be 60.1%. Based on phenotypic, chemotaxonomic, phylogenetic properties and genomic comparison, it is concluded that strain 1N-3T represents a novel species of the genus Phyllobacterium, for which the name Phyllobacterium phragmitis sp. nov. is proposed. The type strain is 1N-3T (=KCTC 62183T =ACCC 60071T).

Sphingomonas deserti sp. nov., isolated from Mu Us Sandy Land soil.

A Gram-stain-negative, rod-shaped bacterium, designated as strain GL-C-18T, was isolated from soil sample collected at Mu Us Sandy Land, China, and its taxonomic position was investigated using a polyphasic approach. Growth was observed in the presence of 0-1 % (w/v) NaCl (optimum, 0 %), pH 6.0-9.0 (optimum, pH 7.0-8.0) and 20-37 °C. On the basis of 16S rRNA gene sequence similarity, strain GL-C-18T belonged to the family Sphingomonadaceae and was most closely related to Sphingosinicella vermicomposti YC7378T (95.7 %), Sphingomonas oligophenolica S213T (95.0 %) and Sphingobium boeckii 301T (94.8 %). The draft genome of strain GL-C-18T was 6.09 Mb, and the G+C content was 66.0 %. The average nucleotide identity value to Sphingosinicella vermicomposti YC7378T was 83.7 %. The predominant respiratory quinone was Q-10. The major fatty acids were C18 : 1ω7c, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), C16:0 and C14 : 0 2OH. The main polar lipids were sphingoglycolipid, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and phosphatidylcholine. On the basis of chemotaxonomic, phylogenetic and phenotypic evidence, strain GL-C-18T represents a novel species of the genus Sphingomonas, for which the name Sphingomonasdeserti sp. nov. is proposed. The type strain is GL-C-18T (=ACCC 60076T=KCTC 62411T).

Mesorhizobium ephedrae sp. nov. isolated from the roots of Ephedra przewalskii in Kumtag desert.

Strain 6GN-30T, a Gram-stain-negative, aerobic, non-spore-forming, rod-shaped, motile bacterium was isolated from Ephedra sinica roots in the Kumtag Desert. On the basis of the 16S rRNA gene sequence, the isolate represented a member of the genus Mesorhizobium of the family Phyllobacteriaceae. The results of a phylogenetic analysis indicated that 6GN-30T was phylogenetically related to Mesorhizobium soliNHI-8T. Strain 6GN-30T grew at a salinity of 0-1.0 % (w/v) NaCl (with optimum growth in the absence of NaCl), pH 6.0-9.0 (optimum 7.0-8.0) and 15-45 °C. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), C19 : 0cyclo ω8c, iso-C17 : 0, C18 : 0, and C16 : 0. The draft genome of 6GN-30T was 6.11 Mb long, with a DNA G+C content of 66.4 mol%. The average nucleotide identity to M. soliNHI-8T was 84.32 %. The strain contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine,aminophospholipids and phospholipids. The chemotaxonomic, phylogenetic and phenotypic data indicate that 6GN-30T represents a novel species of the genus Mesorhizobiumfor which the name Mesorhizobiumephedrae sp. nov. is proposed. The type strain is 6GN-30T (=ACCC 60073T=KCTC 62410T).

Zobellella endophytica sp. nov., isolated from the roots of Phragmites communis in the Kumtag Desert.

A Gram-negative, aerobic, non-spore-forming, rod-shaped, motile bacterium, named strain 59N8T, was isolated from Phragmites communis roots in the Kumtag Desert. Phylogenetic analysis based on the 16S rRNA gene sequence showed that the isolate belongs to the genus Zobellella within the family Aeromonadaceae. The analysis showed that strain 59N8T was most closely related to Zobellella taiwanensis ZT1T. The average nucleotide identity value with Zobellella taiwanensis ZT1T was 88.2 %, and the digital DNA-DNA hybridization value was 29.7±2.4 %, which was calculated using the Genome-to-Genome Distance Calculator. The G+C content of strain 59N8T was 62.8 mol%. Strain 59N8T grew at 0-5 % (w/v) NaCl (optimum, 0-4 %), pH 6.0-9.0 (optimum, 7.0-8.0) and at 10-45 °C. The major cellular fatty acids were summed feature 8 (C18 : 1ω7c/C18 : 1ω6c), summed feature 3 (C16 : 1ω7c/C16 : 1ω6c) and C16 : 0. The major polar lipids in strain 59N8T were phosphatidylethanolamine and phosphatidylglycerol. Based on the chemotaxonomic, phylogenetic and phenotypic data, strain 59N8T represents a novel species in the genus Zobellella, for which the name Zobellellaendophytica sp. nov. is proposed. The type strain is 59N8T (=ACCC 60074T=KCTC 62456T).

Sphingobacterium haloxyli sp. nov., an endophytic bacterium isolated from Haloxylon ammodendron stems in Kumtag desert.

A Gram-stain-negative, non-motile, aerobic, non-spore-forming, rod-shaped, bacterial strain, designated 5JN-11T, was isolated from Haloxylonammodendron stems in Kumtag desert, Xinjiang province, China. Strain 5JN-11T grew at salinities of 0-6 % (w/v; optimum 0-2 %), a pH of 7.0-9.0 (pH 7.0-8.0) and temperatures of 20-42 °C (28-30 °C). Based on 16S rRNA gene sequences, the strain was designated a member of the genus Sphingobacterium and the phylogenetic analysis showed that strain 5JN-11T shared the highest similarity to Sphingobacterium gobiense H7T, followed by Sphingobacterium chuzhouense DH-5T and Sphingobacterium arenae H-12T. The unfinished draft genome of strain 5JN-11T was 4.69 Mb. The G+C content of strain 5JN-11T was 42.8 mol%. The average nucleotide identity to S. gobiense H7T was 90.5 %. The respiratory quinone was MK-7, and the major polar lipids were phosphatidylethanolamine and phosphoglycolipid. The predominant cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C15 : 0 and iso-C17 : 0 3-OH. On the basis of phenotypic, genotypic and phylogenetic evidence, strain 5JN-11T represents a novel species in the genus Sphingobacterium, for which the name Sphingobacteriumhaloxyli sp. nov. is proposed. The type strain is 5JN-11T (=ACCC 60072T=KCTC 62457T).

Comparative Analyses of Anatomical Structure, Phytohormone Levels, and Gene Expression Profiles Reveal Potential Dwarfing Mechanisms in Shengyin Bamboo (Phyllostachys edulis f. tubaeformis).

Moso bamboo (Phyllostachys edulis) is one of the most important bamboo species in China and the third most important plant species for timber production. However, the dwarf variant of moso bamboo, P. edulis f. tubaeformis (shengyin bamboo), which has shortened internodes, is not well studied. We used anatomical, hormonal, and transcriptomic approaches to study internode shortening and shoot growth in dwarf shengyin and wild moso bamboo. Phenotypic and anatomical observations showed that dwarfing in shengyin bamboo is due to reduced internode length, and the culm fibers in shengyin bamboo are significantly shorter and thicker than in wild moso bamboo. We measured the levels of endogenous hormones in the internodes and found that shengyin bamboo had lower levels of four hormones while two others were higher in wild moso bamboo. Comparative transcriptome analyses revealed a potential regulating mechanism for internode length involving genes for cell wall loosening-related enzymes and the cellulose and lignin biosynthesis pathways. Genes involved in hormone biosynthesis and signal transduction, especially those that showed significant differential expression in the internodes between shengyin and wild moso bamboo, may be important in determining the shortened internode phenotype. A hypothesis involving possible cross-talk between phytohormone signaling cues and cell wall expansion leading to dwarfism in shengyin bamboo is proposed. The results presented here provide a comprehensive exploration of the biological mechanisms that determine internode shortening in moso bamboo.

Genome-wide analysis of day/night DNA methylation differences in Populus nigra.

DNA methylation is an important mechanism of epigenetic modification. Methylation changes during stress responses and developmental processes have been well studied; however, their role in plant adaptation to the day/night cycle is poorly understood. In this study, we detected global methylation patterns in leaves of the black poplar Populus nigra 'N46' at 8:00 and 24:00 by methylated DNA immunoprecipitation sequencing (MeDIP-seq). We found 10,027 and 10,242 genes to be methylated in the 8:00 and 24:00 samples, respectively. The methylated genes appeared to be involved in multiple biological processes, molecular functions, and cellular components, suggesting important roles for DNA methylation in poplar cells. Comparing the 8:00 and 24:00 samples, only 440 differentially methylated regions (DMRs) overlapped with genic regions, including 193 hyper- and 247 hypo-methylated DMRs, and may influence the expression of 137 downstream genes. Most hyper-methylated genes were associated with transferase activity, kinase activity, and phosphotransferase activity, whereas most hypo-methylated genes were associated with protein binding, ATP binding, and adenyl ribonucleotide binding, suggesting that different biological processes were activated during the day and night. Our results indicated that methylated genes were prevalent in the poplar genome, but that only a few of these participated in diurnal gene expression regulation.